Trifoliate orange (Poncirus trifoliata), a deciduous close relative of evergreen Citrus, has important traits for citrus production, including tolerance/resistance to citrus greening disease (Huanglongbing, HLB) and other major diseases, and cold tolerance. It has been one of the most important rootstocks, and one of the most valuable sources of resistance and tolerance genes for citrus. Here we present a high‐quality, chromosome‐scale genome assembly of P. trifoliata. The 264.9‐Mb assembly contains nine chromosomal pseudomolecules with 25 538 protein‐coding genes, covering 97.2% of the estimated gene space. Comparative analyses of P. trifoliata and nine Citrus genomes revealed 605 species‐specific genes and six rapidly evolving gene families in the P. trifoliata genome. Poncirus trifoliata has evolved specific adaptation in the C‐repeat/DREB binding factor (CBF)‐dependent and CBF‐independent cold signaling pathways to tolerate cold. We identified candidate genes within quantitative trait loci for HLB tolerance, and at the loci for resistance to citrus tristeza virus and citrus nematode. Genetic diversity analysis of Poncirus accessions and Poncirus/Citrus hybrids shows a narrow genetic base in the US germplasm collection, and points to the importance of collecting and preserving more natural genetic variation. Two phenotypically divergent Poncirus accessions are found to be clonally related, supporting a previous conjecture that dwarf Flying Dragon originated as a mutant of a non‐dwarfing type. The high‐quality genome reveals features and evolutionary insights of Poncirus, and it will serve as a valuable resource for genetic, genomic and molecular research and manipulation in citrus.

中文翻译：

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三叶橙（Poncirus trifoliata）的染色体尺度参考基因组为柑橘的抗病性、耐冷性和基因组进化提供了见解


枳（ Poncirus trifoliata ）是常绿柑橘的落叶近亲，具有对柑橘黄龙病（黄龙病，HLB）等主要病害的耐/抗性和耐寒性等柑橘生产的重要性状。它是柑橘最重要的砧木之一，也是最有价值的抗性和耐受性基因来源之一。在这里，我们展示了P. trifoliata的高质量、染色体​​规模的基因组组装。 264.9 Mb 的组装体包含 9 个染色体假分子和 25 538 个蛋白质编码基因，覆盖了估计基因空间的 97.2%。对P. trifoliata和 9 个柑橘基因组的比较分析揭示了P. trifoliata基因组中的 605 个物种特异性基因和 6 个快速进化的基因家族。枳实在C 重复/DREB 结合因子( CBF ) 依赖和CBF独立的寒冷信号通路中进化出了特异性适应能力，以耐受寒冷。我们在数量性状基因座内鉴定了 HLB 耐受性的候选基因，以及在柑橘 tristeza 病毒和柑橘线虫抗性基因座上的候选基因。对枳属种质和枳属/柑橘杂交种的遗传多样性分析显示，美国种质库中的遗传基础很窄，并指出了收集和保存更多自然遗传变异的重要性。两个表型不同的枳属品种被发现具有克隆相关性，支持了之前的猜想，即矮飞龙起源于非矮化类型的突变体。 高质量的基因组揭示了枳属的特征和进化见解，它将成为柑橘遗传、基因组和分子研究和操作的宝贵资源。